S100P

S100 calcium binding protein P, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 4:6693878-6697170

Links

ENSG00000163993 ∙ NCBI:6286 ∙ OMIM:600614 ∙ HGNC:10504 ∙ Uniprot:P25815 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100P gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in S100P

This is a list of pathogenic ClinVar variants found in the S100P region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-6693951-G-A		not specified	Uncertain significance (May 24, 2023)
4-6693955-T-C		not specified	Uncertain significance (Mar 18, 2024)
4-6693994-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-6694007-G-A			Benign (May 24, 2018)
4-6694020-A-G		not specified	Uncertain significance (May 26, 2022)
4-6694043-G-C		not specified	Uncertain significance (Jan 17, 2023)
4-6696929-A-G		not specified	Uncertain significance (May 11, 2022)
4-6696945-A-G		not specified	Uncertain significance (May 23, 2023)
4-6697022-G-C		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100P	protein_coding	protein_coding	ENST00000296370	2	4102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0333	0.630	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.378	63	55.1	1.14	0.00000302	624
Missense in Polyphen		19	13.687	1.3881		170
Synonymous	0.282	22	23.7	0.926	0.00000153	179
Loss of Function	0.295	2	2.50	0.799	1.93e-7	20

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000588	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as calcium sensor and contribute to cellular calcium signaling. In a calcium-dependent manner, functions by interacting with other proteins, such as EZR and PPP5C, and indirectly plays a role in physiological processes like the formation of microvilli in epithelial cells. May stimulate cell proliferation in an autocrine manner via activation of the receptor for activated glycation end products (RAGE). {ECO:0000269|PubMed:14617629, ECO:0000269|PubMed:19111582, ECO:0000269|PubMed:22399290}.
• Pathway: Gastric Cancer Network 1;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.273
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: response to organic substance;neutrophil degranulation;endothelial cell migration
• Cellular component: extracellular region;nucleus;cytoplasm;nuclear body;microvillus membrane;secretory granule lumen;extracellular exosome
• Molecular function: magnesium ion binding;calcium ion binding;protein binding;protein homodimerization activity;cadherin binding;transition metal ion binding;calcium-dependent protein binding;RAGE receptor binding